Data underlying Figure 5 (Dengue incidence in intervention and control areas, before and after the Wolbachia intervention) and Figure 6 (Laboratory-confirmed dengue cases in intervention and control areas, before and after the Wolbachia intervention), in Indriani et al (2020) Gates Open Research (submitted). Hospitalised dengue haemorrhagic fever (DHF; since 2006) and dengue fever (DF; since 2017) cases are notified to the Yogyakarta District Health Office. Standard Diagnostics Dengue Duo rapid diagnostic kits for the detection of dengue virus NS1 antigen and IgM/IgG antibody have been used at the discretion of clinic staff as part of routine clinical care in primary care clinics throughout Yogyakarta city since March 2016.